Frontpage of Novus Atlas sinensis, by Martino Martini, Amsterdam, 1655.​Soon after Martini's arrival to China, the Ming capital Beijing fell to Li Zicheng's rebels (April, 1644) and then to the Manchus, and the last legitimate Ming emperor, the Chongzhen Emperor, hanged himself. Down in Zhenjiang, Martini continued working with the short-lived regime of Zhu Yujian, Prince of Tang, who set himself up as the (Southern) Ming Longwu Emperor. Soon enough, the Manchu troops reached Zhejiang. According to Martini's own report (which appeared in some editions of his De bello tartarico), the Jesuit was able to switch his allegiance to China's new masters in an easy enough, but bold, way. When Wenzhou, in southern Zhejiang, where Martini happened to be on a mission for Zhu Yujian, was besieged by the Manchus and was about to fall, the Jesuit decorated the house where he was staying with a large red poster with seven characters saying, "Here lives a doctor of the divine Law who has come from the Great West". Under the poster he set up tables with European books, astronomical instruments, etc., surrounding an altar with an image of Jesus. When the Manchu troops arrived, their commander was sufficiently impressed with the display to approach Martini politely and ask if he'd like to switch his loyalty to the new Qing Dynasty. Martini agreed, and had his head shaved in the Manchu way, and his Chinese dress and hat replaced with Manchu-styles ones. The Manchus then allowed him to return to his Hangzhou church, and provided him and the Hangzhou Christian community with necessary protection.[

The Chinese Rites affairIn 1651 Martini left China for Rome as the Delegate of the Chinese Mission Superior. He took advantage of the long, adventurous voyage (going first to the Philippines, from thence on a Dutch privateer to Bergen, Norway,[ which he reached on 31 August 1653, and then to Amsterdam). Further, and still on his way to Rome, he met printers in Antwerp,Vienna and Munich to submit to them historical and cartographic data he had prepared. The works were printed and made him famous.When passing through Leyden, Martini was met by Jacobus Golius, a scholar of Arabic and Persian at the university there. Golius did not know Chinese, but had read about "Cathay" in Persian books, and wanted to verify the truth of the earlier reports of Jesuits such as Matteo Ricci and Bento de Góis who believed that Cathay is the same place as China where they lived or visited. Golius was familiar with the discussion of the "Cathayan" calendar in Zij-i Ilkhani, a work by the Persian astronomer Nasir al-Din al-Tusi, completed in 1272. When Golius met Martini (who, of course knew no Persian), the two scholars found that the names of the 12 divisions into which, according to Nasir al-Din, the "Cathayans" were dividing the day, as well as those of the 24 sections of the year reported by Nasir al-Din matched those that Martini had learned in China. The story, soon published by Martini in the "Additamentum" to his Atlas of China, seemed to have finally convinced most Europeans scholars that China and Cathay were the same.[4]On his way to Rome, Martini met his then 10-year-old cousin Eusebio Kino who later became another famed Jesuitmissionary explorer and the world-renowned cartographer of New Spain.In the spring of 1655 Martini reached Rome. There, in Rome, was the most difficult part of his journey. He had brought along (for the Holy Office of the Church) a long and detailed communication from the Jesuit missionaries in China, in defence of their inculturated missionary and religious approach: the so-called Chinese Rites (Veneration of ancestors, and other practices allowed to new Christians). Discussions and debates took place for five months, at the end of which thePropaganda Fide issued a decree in favour of the Jesuits (23 March 1656). A battle was won, but the controversy did not abate.

WorksA European artist's impression of a Manchu warrior devastating China, from the title page of Martini's Regni Sinensis a Tartaris devastati enarratio. Modern historians (e.g. Pamela Kyle Crossley in The Manchu, or D.E. Mungello) note the discrepancy between the picture and the content of the book; e.g., the severed head held by the warrior has a queue, which is a Manchu hairstyle (also imposed by Manchu on the population of conquered China), and is not likely to be had by a Ming loyalist

Martini's most important work is Novus Atlas Sinensis, which appeared as part of volume 10 of Joan Blaeu's Atlas Maior (Amsterdam 1655). This work, a folio with 17 maps and 171 pages of text was, in the words of the early 20th-century German geographer Ferdinand von Richthofen, the most complete geographical description of China that we possess, and through which Martini has become the father of geographical learning on China. The French Jesuits of the time concurred, saying that even du Halde's monumental Description…de la Chine did not fully supersede Martini's work.[8] (A Scan of the maps of the atlas (not very high resolution), can be seen at the National Library of Australia web site; a very high quality zoomable scan of the maps, at Gallica.bnf.fr).

Of the great chronological work which Martini had planned, and which was to comprise the whole Chinese history from the earliest age, only the first part appeared: Sinicæ Historiæ Decas Prima (Munich 1658), which reached until the birth of Jesus.

His De Bello Tartarico Historia (Antwerp 1654) is also important as Chinese history, for Martini himself had lived through the frightful occurrences which brought about the overthrow of the ancient Ming dynasty. The works have been repeatedly published and translated into different languages. There is also a later version, entitled Regni Sinensis a Tartaris devastati enarratio(1661); compared to the original De Bello Tartarica Historia, it has some additions, such as an index.

Besides these, Martini wrote a series of theological and apologetical works in Chinese, including a De Amicitia (Hangzhou, 1661) that could have been the first anthology of Western authors available in China (Martini's selection fished mainly into Roman and Greek writings).

Several works, among them a Chinese translation of the works of Francisco Suarez, which has not been found yet.

Grammatica Linguae Sinensis: 1652-1653. The first manuscript grammar of Mandarin Chinese and the first grammar of Chinese language ever printed and published in M. Thévenot Relations des divers voyages curieux (1696),[9]